SoroushVahidi/scidocs huggingface dataset:
Innovating with Concept Mapping
(2016)

Student-generated concept maps (Cmaps) have been the preferred choice to design assessment tasks, which are time-consuming in real classroom settings. We have proposed the use of Cmap with errors (elaborated by teachers) to develop assessment tasks, as a way to address the logistical practicality obstacles usually found in classrooms. This paper compared two different tasks, finding the errors and judging the selected propositions in Cmap with errors, exploring two topics with different levels of difficulty. Our results confirmed Cmap with errors as a straightforward approach to include concept mapping into the classroom routine to foster the pedagogic resonance (the bridge between teacher knowledge and student learning), which is critical for motivating students to learn meaningfully. Moreover, Cmaps with errors are also amenable for on-line learning platforms. Future works of our research group will develop an automated process for evaluation and feedback using the task formats presented in this paper.
Natural Language Processing for Question Answering ( NLP 4
(2015)

The recent developments in Question Answering have kept with open-domain questions and collections, sometimes argued as being more di fficult than narrow domain-focused questions and corpora. The biomedical field is indeed a specialized domain; however, its scope is fairly broad, so that considering a biomedical QA task is not necessarily such a simplification over open-domain QA as represented in the recent TREC evaluations. We shall try to characterize salient aspects of biomedical QA as well as to give a short review of useful resources to address this task.
Examining the critical success factors in the adoption of enterprise resource planning
(2008)

This paper presents a literature review of the critical success factors (CSFs) in the implementation of enterprise resource planning (ERP) across 10 different countries/regions. The review covers journals, conference proceedings, doctoral dissertation, and textbooks from these 10 different countries/regions. Through a review of the literature, 18 CSFs were identified, with more than 80 sub-factors, for the successful implementation of ERP. The findings of our study reveal that ‘appropriate business and IT legacy systems’, ‘business plan/vision/goals/justification’, ‘business process reengineering’, ‘change management culture and programme’, ‘communication’, ‘ERP teamwork and composition’, ‘monitoring and evaluation of performance’, ‘project champion’, ‘project management’, ‘software/system development, testing and troubleshooting’, ‘top management support’, ‘data management’, ‘ERP strategy and implementation methodology’, ‘ERP vendor’, ‘organizational characteristics’, ‘fit between ERP and business/process’, ‘national culture’ and ‘country-related functional requirement’ were the commonly extracted factors across these 10 countries/regions. In these 18 CSFs, ‘top management support’ and ‘training and education’ were the most frequently cited as the critical factors to the successful implementation of ERP systems. # 2008 Elsevier B.V. All rights reserved.
Using Quality Models in Software Package Selection
(2003)

0 7 4 0 7 4 5 9 / 0 3 / $ 1 9 . 0 0 © 2 0 0 3 I E E E All the methodologies that have been proposed recently for choosing software packages compare user requirements with the packages’ capabilities.3–5 There are different types of requirements, such as managerial, political, and, of course, quality requirements. Quality requirements are often difficult to check. This is partly due to their nature, but there is another reason that can be mitigated, namely the lack of structured and widespread descriptions of package domains (that is, categories of software packages such as ERP systems, graphical or data structure libraries, and so on). This absence hampers the accurate description of software packages and the precise statement of quality requirements, and consequently overall package selection and confidence in the result of the process. Our methodology for building structured quality models helps solve this drawback. (See the “Related Work” sidebar for information about other approaches.) A structured quality model for a given package domain provides a taxonomy of software quality features, and metrics for computing their value. Our approach relies on the International Organization for Standardization and International Electrotechnical Commission 9126-1 quality standard,6 which we selected for the following reasons:
An AI Approach to Automatic Natural Music Transcription
(2017)

Automatic music transcription (AMT) remains a fundamental and difficult problem in music information research, and current music transcription systems are still unable to match human performance. AMT aims to automatically generate a score representation given a polyphonic acoustical signal. In our project, we approach the AMT problem on two fronts: acoustic modeling to identify pitches from a frame of audio, and establishing a score generation model to convert exact piano roll representations of audio into more ‘natural’ sheet music. We build an end to end pipeline that aims to convert .wav classical piano audio files into a ‘natural’ score representation.
COMPARISON OF LOSSLESS DATA COMPRESSION ALGORITHMS FOR TEXT DATA
(2010)

Data compression is a common requirement for most of the computerized applications. There are number of data compression algorithms, which are dedicated to compress different data formats. Even for a single data type there are number of different compression algorithms, which use different approaches. This paper examines lossless data compression algorithms and compares their performance. A set of selected algorithms are examined and implemented to evaluate the performance in compressing text data. An experimental comparison of a number of different lossless data compression algorithms is presented in this paper. The article is concluded by stating which algorithm performs well for text data.
A Simple and Accurate Syntax-Agnostic Neural Model for Dependency-based Semantic Role Labeling
(2017)

We introduce a simple and accurate neural model for dependency-based semantic role labeling. Our model predicts predicate-argument dependencies relying on states of a bidirectional LSTM encoder. The semantic role labeler achieves competitive performance on English, even without any kind of syntactic information and only using local inference. However, when automatically predicted partof-speech tags are provided as input, it substantially outperforms all previous local models and approaches the best reported results on the English CoNLL2009 dataset. We also consider Chinese, Czech and Spanish where our approach also achieves competitive results. Syntactic parsers are unreliable on out-of-domain data, so standard (i.e., syntactically-informed) SRL models are hindered when tested in this setting. Our syntax-agnostic model appears more robust, resulting in the best reported results on standard out-of-domain test sets.
Walking on foot to explore a virtual environment with uneven terrain
(2015)

In this work we examine people's ability to maintain spatial awareness of an HMD--based immersive virtual environment when the terrain of the virtual world does not match the real physical world in which they are locomoting. More specifically, we examine what happens when a subject explores a hilly virtual environment while physically walking in a flat room. In our virtual environments, subjects maintain their height (or distance to the ground plane) at all times. In the experiment described in this work, we directly compare spatial orientation in a flat virtual environment to two variations of a hilly virtual environment. Interestingly, we find that subjects' spatial awareness of the environment is improved with the addition of uneven terrain.
The emergence of lncRNAs in cancer biology.
(2011)

The discovery of numerous noncoding RNA (ncRNA) transcripts in species from yeast to mammals has dramatically altered our understanding of cell biology, especially the biology of diseases such as cancer. In humans, the identification of abundant long ncRNA (lncRNA) >200 bp has catalyzed their characterization as critical components of cancer biology. Recently, roles for lncRNAs as drivers of tumor suppressive and oncogenic functions have appeared in prevalent cancer types, such as breast and prostate cancer. In this review, we highlight the emerging impact of ncRNAs in cancer research, with a particular focus on the mechanisms and functions of lncRNAs.
Action Reaction Learning : Analysis and Synthesis of Human Behaviour
(1998)

We propose Action-Reaction Learning as an approach for analyzing and synthesizing human behaviour. This paradigm uncovers causal mappings between past and future events or between an action and its reaction by observing time sequences. We apply this method to analyze human interaction and to subsequently synthesize human behaviour. Using a time series of perceptual measurements, a system automatically uncovers a mapping between gestures from one human participant (an action) and a subsequent gesture (a reaction) from another participant. A probabilistic model is trained from data of the human interaction using a novel estimation technique, Conditional Expectation Maximization (CEM). The system drives a graphical interactive character which probabilistically predicts the most likely response to the user's behaviour and performs it interactively. Thus, after analyzing human interaction in a pair of participants, the system is able to replace one of them and interact with a single remaining user.
Vehicle licence plate recognition using super-resolution technique
(2014)

Due to the development of economy and technology, the people's demands on cars are growing and so are the problems, such as finding stolen car, banning violation and parking lot management. It will be time-consuming and low-efficiency if we do those jobs only by human because of the limitation of human being's concentration. Therefore, it has been a popular topic to develop intelligent monitoring system under new video technology within a decade. There are still many rooms for future development and application in the car license detection and recognition fields. For finding stolen car, we can integrate car license detection system and road monitoring system to analyze the videos and trace the objects, so we can gain high-efficiency and low-cost results. For parking lot management system, we can have the result of access management and automatic charge to reduce the human resource through car license recognition system. Automated toll of highway can be done through car license recognition system as well. Because the car license recognition system is mostly applied to security monitoring field and business purposes, the demand of the accuracy is quite strict. There are causes which make the inaccuracy of the license recognition, such as the lack of video resolution, too small license due to the distance and the light and shadow. We will discuss the license recognition system and how to use apply the super-resolution to overcome those above problems.
PubChem Substance and Compound databases
(2016)

PubChem (https://pubchem.ncbi.nlm.nih.gov) is a public repository for information on chemical substances and their biological activities, launched in 2004 as a component of the Molecular Libraries Roadmap Initiatives of the US National Institutes of Health (NIH). For the past 11 years, PubChem has grown to a sizable system, serving as a chemical information resource for the scientific research community. PubChem consists of three inter-linked databases, Substance, Compound and BioAssay. The Substance database contains chemical information deposited by individual data contributors to PubChem, and the Compound database stores unique chemical structures extracted from the Substance database. Biological activity data of chemical substances tested in assay experiments are contained in the BioAssay database. This paper provides an overview of the PubChem Substance and Compound databases, including data sources and contents, data organization, data submission using PubChem Upload, chemical structure standardization, web-based interfaces for textual and non-textual searches, and programmatic access. It also gives a brief description of PubChem3D, a resource derived from theoretical three-dimensional structures of compounds in PubChem, as well as PubChemRDF, Resource Description Framework (RDF)-formatted PubChem data for data sharing, analysis and integration with information contained in other databases.
Adam: A Method for Stochastic Optimization
(2015)

We introduce Adam, an algorithm for first-order gradient-based optimization of stochastic objective functions, based on adaptive estimates of lower-order moments. The method is straightforward to implement, is computationally efficient, has little memory requirements, is invariant to diagonal rescaling of the gradients, and is well suited for problems that are large in terms of data and/or parameters. The method is also appropriate for non-stationary objectives and problems with very noisy and/or sparse gradients. The hyper-parameters have intuitive interpretations and typically require little tuning. Some connections to related algorithms, on which Adam was inspired, are discussed. We also analyze the theoretical convergence properties of the algorithm and provide a regret bound on the convergence rate that is comparable to the best known results under the online convex optimization framework. Empirical results demonstrate that Adam works well in practice and compares favorably to other stochastic optimization methods. Finally, we discuss AdaMax, a variant of Adam based on the infinity norm.
Probabilistic Principal Component Analysis
(1997)

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Stochastic Variational Inference
(2013)

We develop stochastic variational inference, a scalable algorithm for approximating posterior distributions. We develop this technique for a large class of probabilistic models and we demonstrate it with two probabilistic topic models, latent Dirichlet allocation and the hierarchical Dirichlet process topic model. Using stochastic variational inference, we analyze several large collections of documents: 300K articles from Nature, 1.8M articles from The New York Times, and 3.8M articles from Wikipedia. Stochastic inference can easily handle data sets of this size and outperforms traditional variational inference, which can only handle a smaller subset. (We also show that the Bayesian nonparametric topic model outperforms its parametric counterpart.) Stochastic variational inference lets us apply complex Bayesian models to massive data sets.
PILCO: A Model-Based and Data-Efficient Approach to Policy Search
(2011)

In this paper, we introduce pilco, a practical, data-efficient model-based policy search method. Pilco reduces model bias, one of the key problems of model-based reinforcement learning, in a principled way. By learning a probabilistic dynamics model and explicitly incorporating model uncertainty into long-term planning, pilco can cope with very little data and facilitates learning from scratch in only a few trials. Policy evaluation is performed in closed form using state-ofthe-art approximate inference. Furthermore, policy gradients are computed analytically for policy improvement. We report unprecedented learning efficiency on challenging and high-dimensional control tasks.
Adaptive Subgradient Methods for Online Learning and Stochastic Optimization
(2010)

We present a new family of subgradient methods that dynamica lly incorporate knowledge of the geometry of the data observed in earlier iterations to perfo rm more informative gradient-based learning. Metaphorically, the adaptation allows us to find n eedles in haystacks in the form of very predictive but rarely seen features. Our paradigm stems fro m recent advances in stochastic optimization and online learning which employ proximal funct ions to control the gradient steps of the algorithm. We describe and analyze an apparatus for adap tively modifying the proximal function, which significantly simplifies setting a learning rate nd results in regret guarantees that are provably as good as the best proximal function that can be cho sen in hindsight. We give several efficient algorithms for empirical risk minimization probl ems with common and important regularization functions and domain constraints. We experimen tally study our theoretical analysis and show that adaptive subgradient methods outperform state-o f-the-art, yet non-adaptive, subgradient algorithms.
A 14-mW 6.25-Gb/s Transceiver in 90-nm CMOS
(2007)

This paper describes a 6.25-Gb/s 14-mW transceiver in 90-nm CMOS for chip-to-chip applications. The transceiver employs a number of features for reducing power consumption, including a shared LC-PLL clock multiplier, an inductor-loaded resonant clock distribution network, a low- and programmable-swing voltage-mode transmitter, software-controlled clock and data recovery (CDR) and adaptive equalization within the receiver, and a novel PLL-based phase rotator for the CDR. The design can operate with channel attenuation of -15 dB or greater at a bit-error rate of 10-15 or less, while consuming less than 2.25 mW/Gb/s per transceiver.
Limbic-cortical dysregulation: a proposed model of depression.
(1997)

A working model of depression implicating failure of the coordinated interactions of a distributed network of limbic-cortical pathways is proposed. Resting state patterns of regional glucose metabolism in idiopathic depressed patients, changes in metabolism with antidepressant treatment, and blood flow changes with induced sadness in healthy subjects were used to test and refine this hypothesis. Dorsal neocortical decreases and ventral paralimbic increases characterize both healthy sadness and depressive illness; concurrent inhibition of overactive paralimbic regions and normalization of hypofunctioning dorsal cortical sites characterize disease remission. Normal functioning of the rostral anterior cingulate, with its direct connections to these dorsal and ventral areas, is postulated to be additionally required for the observed reciprocal compensatory changes, since pretreatment metabolism in this region uniquely predicts antidepressant treatment response. This model is offered as an adaptable framework to facilitate continued integration of clinical imaging findings with complementary neuroanatomical, neurochemical, and electrophysiological studies in the investigation of the pathogenesis of affective disorders.
Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents.
(2004)

We describe here a multiplexed protein quantitation strategy that provides relative and absolute measurements of proteins in complex mixtures. At the core of this methodology is a multiplexed set of isobaric reagents that yield amine-derivatized peptides. The derivatized peptides are indistinguishable in MS, but exhibit intense low-mass MS/MS signature ions that support quantitation. In this study, we have examined the global protein expression of a wild-type yeast strain and the isogenic upf1Delta and xrn1Delta mutant strains that are defective in the nonsense-mediated mRNA decay and the general 5' to 3' decay pathways, respectively. We also demonstrate the use of 4-fold multiplexing to enable relative protein measurements simultaneously with determination of absolute levels of a target protein using synthetic isobaric peptide standards. We find that inactivation of Upf1p and Xrn1p causes common as well as unique effects on protein expression.
An Efficient Certificateless Encryption for Secure Data Sharing in Public Clouds
(2014)

We propose a mediated certificateless encryption scheme without pairing operations for securely sharing sensitive information in public clouds. Mediated certificateless public key encryption (mCL-PKE) solves the key escrow problem in identity based encryption and certificate revocation problem in public key cryptography. However, existing mCL-PKE schemes are either inefficient because of the use of expensive pairing operations or vulnerable against partial decryption attacks. In order to address the performance and security issues, in this paper, we first propose a mCL-PKE scheme without using pairing operations. We apply our mCL-PKE scheme to construct a practical solution to the problem of sharing sensitive information in public clouds. The cloud is employed as a secure storage as well as a key generation center. In our system, the data owner encrypts the sensitive data using the cloud generated users' public keys based on its access control policies and uploads the encrypted data to the cloud. Upon successful authorization, the cloud partially decrypts the encrypted data for the users. The users subsequently fully decrypt the partially decrypted data using their private keys. The confidentiality of the content and the keys is preserved with respect to the cloud, because the cloud cannot fully decrypt the information. We also propose an extension to the above approach to improve the efficiency of encryption at the data owner. We implement our mCL-PKE scheme and the overall cloud based system, and evaluate its security and performance. Our results show that our schemes are efficient and practical.
Clustal W and Clustal X version 2.0
(2007)

SUMMARY
The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems.


AVAILABILITY
The programs can be run on-line from the EBI web server: http://www.ebi.ac.uk/tools/clustalw2. The source code and executables for Windows, Linux and Macintosh computers are available from the EBI ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/